Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids

Trait associations in the pangenome of pigeon pea ( Cajanus cajan )

(2020) Junliang Zhao et al.   PLANT BIOTECHNOLOGY JOURNAL

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

(2020) Z. Jeffrey Chen et al.   NATURE GENETICS

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

A copia-like retrotransposon insertion in the upstream region of the SHATTERPROOF1 gene, BnSHP1.A9, is associated with quantitative variation in pod shattering resistance in oilseed rape

(2020) Jia Liu et al.   JOURNAL OF EXPERIMENTAL BOTANY

A high‐quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance

(2020) Xuequn Chen et al.   PLANT BIOTECHNOLOGY JOURNAL

Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement

(2019) Kun Lu et al.   Nature Communications

Origin and evolution of the octoploid strawberry genome

(2019) Patrick P. Edger et al.   NATURE GENETICS

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

(2019) Lei Gao et al.   NATURE GENETICS

Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus

(2019) Hong An et al.   Nature Communications

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

(2018) Qiang Zhao et al.   NATURE GENETICS

PANNZER2: a rapid functional annotation web server

(2018) Petri Törönen et al.   NUCLEIC ACIDS RESEARCH

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

(2018) Bhavna Hurgobin et al.   PLANT BIOTECHNOLOGY JOURNAL

Homoeolog expression bias and expression level dominance in resynthesized allopolyploid Brassica napus

(2018) Jian Wu et al.   BMC GENOMICS

Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome

(2018) Philipp E Bayer et al.   PLANT BIOTECHNOLOGY JOURNAL

Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies

(2018) Lei Zhang et al.   Horticulture Research

Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence

(2018) Dezhi Wu et al.   Molecular Plant

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Insight into the evolution and functional characteristics of the pan‐genome assembly from sesame landraces and modern cultivars

(2018) Jingyin Yu et al.   PLANT BIOTECHNOLOGY JOURNAL

Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower

(2017) Patrick P. Edger et al.   PLANT CELL

The pangenome of hexaploid bread wheat

(2017) Juan D. Montenegro et al.   PLANT JOURNAL

Evolution of protein-protein interaction networks in yeast

(2017) Andrew Schoenrock et al.   PLoS One

Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas

(2017) Alexandre Pelé et al.   PLoS Genetics

RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants

(2016) Pingchuan Li et al.   BMC GENOMICS

Distinct subgenome stabilities in synthesized Brassica allohexaploids

(2016) Jiannan Zhou et al.   THEORETICAL AND APPLIED GENETICS

The pangenome of an agronomically important crop plant Brassica oleracea

(2016) Agnieszka A. Golicz et al.   Nature Communications

Helitron-like transposons contributed to the mating system transition from out-crossing to self-fertilizing in polyploid Brassica napus L.

(2016) Changbin Gao et al.   Scientific Reports

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis

(2015) A. S. Mason et al.   GENETICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Species-wide genome sequence and nucleotide polymorphisms from the model allopolyploid plant Brassica napus

(2015) Thomas Schmutzer et al.   Scientific Data

Self-incompatibility in Brassicaceae crops: lessons for interspecific incompatibility

(2014) Hiroyasu Kitashiba et al.   BREEDING SCIENCE

Gene loss in the fungal canola pathogen Leptosphaeria maculans

(2014) Agnieszka A. Golicz et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

(2014) B. Chalhoub et al.   SCIENCE

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

(2014) Isobel AP Parkin et al.   GENOME BIOLOGY

Genome triplication drove the diversification of Brassica plants

(2014) Feng Cheng et al.   Horticulture Research

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Dispersion and domestication shaped the genome of bread wheat

(2013) Paul J. Berkman et al.   PLANT BIOTECHNOLOGY JOURNAL

GsSRK, a G-type lectin S-receptor-like serine/threonine protein kinase, is a positive regulator of plant tolerance to salt stress

(2012) Xiao-Li Sun et al.   JOURNAL OF PLANT PHYSIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Rapid copy number expansion and recent recruitment of domains in S-receptor kinase-like genes contribute to the origin of self-incompatibility

(2011) Xiaohui Zhang et al.   FEBS Journal

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers

(2010) Charlotte J Allender et al.   BMC PLANT BIOLOGY

Gene copy number evolution during tetraploid cotton radiation

(2010) J Rong et al.   HEREDITY

Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs

(2010) Margaret R. Woodhouse et al.   PLOS BIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The CACTA transposonBot1played a major role inBrassicagenome divergence and gene proliferation

(2008) Karine Alix et al.   PLANT JOURNAL

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY